Analyzing G25 corrdinates of ancient DNA samples using graphs
In [1]:
require(rio)
require(tidyverse)
require(cowplot)
require(gridExtra)
require(dbscan)
require(igraph)
require(tidygraph)
require(ggraph)
require(pals)
Loading required package: cowplot
Attaching package: ‘cowplot’
The following object is masked from ‘package:lubridate’:
stamp
Loading required package: gridExtra
Attaching package: ‘gridExtra’
The following object is masked from ‘package:dplyr’:
combine
Loading required package: dbscan
Attaching package: ‘dbscan’
The following object is masked from ‘package:stats’:
as.dendrogram
Loading required package: igraph
Attaching package: ‘igraph’
The following objects are masked from ‘package:stats’:
decompose, spectrum
The following objects are masked from ‘package:lubridate’:
%--%, union
The following objects are masked from ‘package:dplyr’:
as_data_frame, groups, union
The following objects are masked from ‘package:purrr’:
compose, simplify
The following object is masked from ‘package:tidyr’:
crossing
The following object is masked from ‘package:tibble’:
as_data_frame
The following object is masked from ‘package:base’:
union
Loading required package: tidygraph
Attaching package: ‘tidygraph’
The following object is masked from ‘package:igraph’:
groups
The following object is masked from ‘package:stats’:
filter
The following object is masked from ‘package:rio’:
convert
Loading required package: ggraph
Loading required package: pals
Load the data for modern and ancient G25 population averages
In [2]:
avgs = as_tibble(import("../Genetics/G25/Data/TXT/Global25_PCA_pop_averages_scaled.txt"))
#avgs %>% sample_n(10)
modavgs = as_tibble(import("../Genetics/G25/Data/TXT/Global25_PCA_modern_pop_averages_scaled.txt"))
#modavgs %>% sample_n(10)
Optionally, filter the dataset down
In [3]:
str_extract(avgs$V1,"^\\w+?(?=_)") %>% unique(sort = TRUE)
- 'ARG'
- 'ARM'
- 'AUS'
- 'AUT'
- 'AZE'
- 'Baltic'
- 'BEL'
- 'Bell'
- 'BGR'
- 'BHS'
- 'BLZ'
- 'BRA'
- 'BWA'
- 'CAN'
- 'Canary'
- 'Channel'
- 'CHE'
- 'CHL'
- 'CHN'
- 'CMR'
- 'COG'
- 'Corded'
- 'CUW'
- 'CZE'
- 'DEU'
- 'DNK'
- 'DOM'
- 'EGY'
- 'England'
- 'ETH'
- 'FIN'
- 'FRA'
- 'GEO'
- 'Gepidian'
- 'GRC'
- 'Greater'
- 'GUM'
- 'HRV'
- 'HTI'
- 'HUN'
- 'Hun'
- 'Iberia'
- 'IDN'
- 'IND'
- 'IRL'
- 'IRN'
- 'ISL'
- 'Isle'
- 'ITA'
- 'JPN'
- 'KAZ'
- 'KEN'
- 'KGZ'
- 'KOR'
- NA
- 'LAO'
- 'Levant'
- 'LUX'
- 'MAR'
- 'MDA'
- 'MEX'
- 'MKD'
- 'MNG'
- 'MWI'
- 'MYS'
- 'NLD'
- 'NOR'
- 'NPL'
- 'Orkney'
- 'Ostrogothic'
- 'PAK'
- 'PAN'
- 'PER'
- 'POL'
- 'PYF'
- 'ROU'
- 'RUS'
- 'Saka'
- 'Sargat'
- 'Sarmatian'
- 'Scotland'
- 'Scythian'
- 'SDN'
- 'SRB'
- 'SVK'
- 'SVN'
- 'SWE'
- 'SYR'
- 'THA'
- 'TJK'
- 'TKM'
- 'TON'
- 'TUR'
- 'TWN'
- 'TZA'
- 'UGA'
- 'UKR'
- 'USA'
- 'UZB'
- 'VEN'
- 'VK2020'
- 'VNM'
- 'VUT'
- 'Wales'
- 'Yamnaya'
- 'ZAF'
In [4]:
str_extract(modavgs$V1,"^\\w+?$") %>% unique(sort = TRUE)
- 'Abazin'
- 'Abkhasian'
- 'Abkhasian_Gudauta'
- 'Adygei'
- 'Aeta'
- 'Afrikaner'
- 'Agta'
- 'Ahiska'
- 'Akha'
- 'Akhvakh'
- 'Alawite'
- 'Albanian'
- 'Alevi_Dersim'
- 'Algerian'
- 'Altaian'
- 'Amerindian_North'
- 'Ami'
- 'Andian_A'
- 'Andian_B'
- 'Arain'
- 'Armenian_Aintab'
- 'Armenian_Ararat'
- 'Armenian_Artsakh'
- 'Armenian_Erzurum'
- 'Armenian_Gesaria'
- 'Armenian_Gurin'
- 'Armenian_Hemsheni'
- 'Armenian_Parspatunik'
- 'Armenian_Syunik'
- 'Armenian_Urfa'
- 'Arora'
- 'Ashkenazi_Belarussia'
- 'Ashkenazi_Germany'
- 'Ashkenazi_Lithuania'
- 'Ashkenazi_Poland'
- 'Ashkenazi_Russia'
- 'Ashkenazi_Ukraine'
- 'Assyrian'
- 'Asur'
- 'Atayal'
- 'Australian'
- 'Austrian'
- 'Avar'
- 'Awan'
- 'Aymara'
- 'Azerbaijani_Dagestan'
- 'Azerbaijani_Iran'
- 'Azerbaijani_Republic'
- 'Azerbaijani_Republic_Gabala'
- 'Azerbaijani_Republic_Shaki'
- 'Azerbaijani_Turkey'
- 'Bagvalin'
- 'Bagvalin_o'
- 'Bahun'
- 'Bahun_o'
- 'Bai'
- 'Baiku_Yao_Guizhou'
- 'Bajo'
- 'Baka'
- 'Bakola'
- 'Balija'
- 'Balkar'
- 'Balochi'
- 'Balti'
- 'Balti_o'
- 'Baniya_Gujarat'
- 'Baniya_Punjab'
- 'Baniya_Uttar_Pradesh_Gupta'
- 'Bantu_Kenya'
- NA
- 'Baoan'
- 'Bashkir'
- 'Basque_Araba'
- 'Basque_Baztan'
- 'Basque_Biscay'
- 'Basque_French'
- 'Basque_Gipuzkoa'
- 'Basque_Gipuzkoa_Southwest'
- 'Basque_Lower_Navarre'
- 'Basque_Navarre_Center'
- 'Basque_Navarre_North'
- 'Basque_Roncal'
- 'Basque_Soule'
- 'Basque_Spanish'
- 'Batak'
- 'BedouinA'
- 'BedouinB'
- 'Bedzan'
- 'Belarusian'
- 'BelgianA'
- 'BelgianB'
- 'BelgianC'
- 'Bengali_Bangladesh'
- 'Bengali_Bangladesh_SouthEast'
- 'Bengali_Bangladesh_Sylhet'
- 'Berber_Algeria'
- 'Berber_MAR_ERR'
- 'Berber_MAR_TIZ'
- 'Berber_Tunisia_Chen'
- 'Berber_Tunisia_Sen'
- 'Besermyan'
- 'Bhumihar_Bihar'
- 'Bhumij'
- 'Biaka'
- 'Birhor'
- 'Bitonga'
- 'Blang'
- 'Bolivian_Cochabamba'
- 'Bolivian_LaPaz'
- 'Bolivian_Pando'
- 'Bonan'
- 'Bonda'
- 'Bosnian'
- 'Brahmin_Gujarat'
- 'Brahmin_Gujarat_Audichya'
- 'Brahmin_Gujarat_Bardai'
- 'Brahmin_Gujarat_Nagar'
- 'Brahmin_Gujarat_o'
- 'Brahmin_Himachal_Pradesh_West'
- 'Brahmin_Jammu_Dogra'
- 'Brahmin_Karnataka_Tulu'
- 'Brahmin_Kerala_Nambudiri'
- 'Brahmin_Konkani_Catholic'
- 'Brahmin_Kumaon'
- 'Brahmin_Manipuri'
- 'Brahmin_Rajasthan'
- 'Brahmin_Tamil_Nadu'
- 'Brahmin_Tamil_Nadu_Iyengar'
- 'Brahmin_Tamil_Nadu_Iyer'
- 'Brahmin_Telugu'
- 'Brahmin_Telugu_Niyogi'
- 'Brahmin_Telugu_Vaidiki'
- 'Brahmin_UP_Awadh_Saryupareen'
- 'Brahmin_UP_Kanyakubja'
- 'Brahmin_UP_Lucknow'
- 'Brahmin_UP_Lucknow_o'
- 'Brahmin_Uttar_Pradesh_East'
- 'Brahmin_Uttar_Pradesh_East_o'
- 'Brahmin_West_Bengal'
- 'Brahui'
- 'Bukharian_Jew'
- 'Bulala'
- 'Bulgarian'
- 'Bunt_Kerala'
- 'Burmese'
- 'Burusho'
- 'Buryat'
- 'Cachi'
- 'Cambodian'
- 'Cameroon_Aghem'
- 'Cameroon_Bafut'
- 'Cameroon_Bakoko'
- 'Cameroon_Bangwa'
- 'Cameroon_Mbo'
- 'Chamalin'
- 'Chamar_Uttar_Pradesh'
- 'Chamar_Uttar_Pradesh_o'
- 'Changana'
- 'Changshan_Yao_Guizhou'
- 'Chechen'
- 'Chenchu'
- 'Cherkes'
- 'Chipewyan'
- 'Chopi'
- 'Chukchi'
- 'Chuvash'
- 'Circassian'
- 'Cochin_Jew_A'
- 'Cochin_Jew_B'
- 'Colla'
- 'Cossack_Kuban'
- 'Cossack_Ukrainian'
- 'Cree'
- 'Croatian'
- 'Cypriot'
- 'Czech'
- 'Dai'
- 'Damai'
- 'Danish'
- 'Darginian'
- 'Datog'
- 'Daur'
- 'Dharkar'
- 'Dinka'
- 'Dolgan'
- 'Dong_Guizhou'
- 'Dong_Hunan'
- 'Dongxiang'
- 'Druze'
- 'Dungan'
- 'Dusadh'
- 'Dusun'
- 'Dutch'
- 'Egyptian'
- 'Elmolo'
- 'EmiratiA'
- 'EmiratiB'
- 'EmiratiC'
- 'English'
- 'English_Cornwall'
- ⋯
- 'Russian_Pinezhsky'
- 'Russian_Pskov'
- 'Russian_Ryazan'
- 'Russian_Smolensk'
- 'Russian_Tver'
- 'Russian_Voronez'
- 'Russian_Yaroslavl'
- 'Saami'
- 'Saami_Kola'
- 'Saharawi'
- 'Sakha'
- 'Sakilli'
- 'Salar'
- 'Saliya_Kerala'
- 'Samaritan'
- 'Sandawe'
- 'Santhal'
- 'Sardinian'
- 'Satnami_Chhattisgarh'
- 'Saudi'
- 'SaudiA'
- 'SaudiB'
- 'Scottish'
- 'Selkup'
- 'Sena'
- 'Sengwer'
- 'Sephardic_Jew'
- 'Sephardic_Jew_o'
- 'Serbian'
- 'She'
- 'Sherpa'
- 'Shetlandic'
- 'Shor'
- 'Shor_Khakassia'
- 'Shor_Mountain'
- 'Sicilian_East'
- 'Sicilian_West'
- 'Sindhi'
- 'Sindhi_o'
- 'Slovakian'
- 'Slovenian'
- 'Somali'
- 'Somali_Kenya'
- 'Sorb_Niederlausitz'
- 'Spanish_Alacant'
- 'Spanish_Andalucia'
- 'Spanish_Aragon'
- 'Spanish_Aragon_North'
- 'Spanish_Asturias'
- 'Spanish_Baleares'
- 'Spanish_Barcelones'
- 'Spanish_Biscay'
- 'Spanish_Burgos'
- 'Spanish_Camp_de_Tarragona'
- 'Spanish_Canarias'
- 'Spanish_Cantabria'
- 'Spanish_Castello'
- 'Spanish_Castilla_La_Mancha'
- 'Spanish_Castilla_Y_Leon'
- 'Spanish_Cataluna'
- 'Spanish_Catalunya_Central'
- 'Spanish_Eivissa'
- 'Spanish_Extremadura'
- 'Spanish_Galicia'
- 'Spanish_Girona'
- 'Spanish_La_Rioja'
- 'Spanish_Lleida'
- 'Spanish_Mallorca'
- 'Spanish_Menorca'
- 'Spanish_Murcia'
- 'Spanish_Navarra'
- 'Spanish_Pais_Vasco'
- 'Spanish_Penedes'
- 'Spanish_Pirineu'
- 'Spanish_Soria'
- 'Spanish_Valencia'
- 'Sri_Lankan'
- 'Sudanese'
- 'Surui'
- 'Swedish'
- 'Swiss_French'
- 'Swiss_German'
- 'Swiss_Italian'
- 'Syed_Uttar_Pradesh_West'
- 'Syrian'
- 'Syrian_Jew'
- 'Tabasaran'
- 'Tai_Lue'
- 'Tajik_Ayni'
- 'Tajik_Hisor'
- 'Tajik_Kulob'
- 'Tajik_Yaghnobi'
- 'Talysh_Azerbaijan'
- 'Tamang'
- 'Tamil_Sri_Lanka'
- 'Tarkhan_Muslim'
- 'Tat_Azerbaijan'
- 'Tat_Dagestan_Dzhalgan'
- 'Tat_Dagestan_Nyugdi'
- 'Tatar_Crimean_steppe'
- 'Tatar_Kazan'
- 'Tatar_Lipka'
- 'Tatar_Mishar'
- 'Tatar_Siberian'
- 'Tatar_Siberian_Zabolotniye'
- 'Telugu'
- 'Thai'
- 'Tharu'
- 'Tharu_o1'
- 'Tharu_o2'
- 'Thiyya'
- 'Tibetan_Chamdo'
- 'Tibetan_Gangcha'
- 'Tibetan_Gannan'
- 'Tibetan_Lhasa'
- 'Tibetan_Nagqu'
- 'Tibetan_Shannan'
- 'Tibetan_Shigatse'
- 'Tibetan_Xinlong'
- 'Tibetan_Xunhua'
- 'Tibetan_Yajiang'
- 'Tibetan_Yunnan'
- 'Tikar_South'
- 'Tindal'
- 'Tlingit'
- 'Todzin'
- 'Tripuri'
- 'Tsez_A'
- 'Tsez_B'
- 'Tswa'
- 'Tu'
- 'Tubalar'
- 'Tujia'
- 'Tunisian'
- 'Tunisian_Berber_Matmata'
- 'Tunisian_Berber_Tamezret'
- 'Tunisian_Berber_Zraoua'
- 'Tunisian_Douz'
- 'Tunisian_Jew'
- 'Tunisian_Rbaya'
- 'Turkish_Antalya'
- 'Turkish_Aydin'
- 'Turkish_Balikesir'
- 'Turkish_Deliorman'
- 'Turkish_Denizli'
- 'Turkish_Erzurum'
- 'Turkish_Giresun'
- 'Turkish_Kayseri'
- 'Turkish_Konya'
- 'Turkish_Nevsehir'
- 'Turkish_Rumeli'
- 'Turkish_Sivas'
- 'Turkish_Trabzon'
- 'Turkmen'
- 'Turkmen_Uzbekistan'
- 'Tuvinian'
- 'Tyagi'
- 'Udi'
- 'Udmurt'
- 'Ukrainian_Chernihiv'
- 'Ukrainian_Dnipro'
- 'Ukrainian_Lviv'
- 'Ukrainian_Rivne'
- 'Ukrainian_Sumy'
- 'Ukrainian_Zakarpattia'
- 'Ukrainian_Zhytomyr'
- 'Ukrainian_Zhytomyr_o'
- 'Ulchi'
- 'Umbundu'
- 'Uttar_Pradesh_Scheduled_Castes'
- 'Uygur'
- 'Uzbek'
- 'Vaniya_Kerala'
- 'Velama'
- 'Vellalar'
- 'Vepsian'
- 'Vishwakarma_Kerala'
- 'Vizayan'
- 'Wa'
- 'Welsh'
- 'Wichi'
- 'Xibo'
- 'Yadav_Telugu'
- 'Yakut'
- 'Yao'
- 'Yemenite_Al_Bayda'
- 'Yemenite_Al_Jawf'
- 'Yemenite_Amran'
- 'Yemenite_Dhamar'
- 'Yemenite_Jew'
- 'Yemenite_Mahra'
- 'Yi'
- 'Yoruba'
- 'Yugur'
- 'Yukagir_Forest'
- 'Yukagir_Tundra'
- 'Yukpa'
- 'Yuku'
- 'Zapotec'
- 'Zhuang'
In [25]:
str_extract(modavgs$V1,"^\\w+?$") %>% unique(sort = TRUE) %>% as.character() %>% paste0(collapse = "|")
'Abazin|Abkhasian|Abkhasian_Gudauta|Adygei|Aeta|Afrikaner|Agta|Ahiska|Akha|Akhvakh|Alawite|Albanian|Alevi_Dersim|Algerian|Altaian|Amerindian_North|Ami|Andian_A|Andian_B|Arain|Armenian_Aintab|Armenian_Ararat|Armenian_Artsakh|Armenian_Erzurum|Armenian_Gesaria|Armenian_Gurin|Armenian_Hemsheni|Armenian_Parspatunik|Armenian_Syunik|Armenian_Urfa|Arora|Ashkenazi_Belarussia|Ashkenazi_Germany|Ashkenazi_Lithuania|Ashkenazi_Poland|Ashkenazi_Russia|Ashkenazi_Ukraine|Assyrian|Asur|Atayal|Australian|Austrian|Avar|Awan|Aymara|Azerbaijani_Dagestan|Azerbaijani_Iran|Azerbaijani_Republic|Azerbaijani_Republic_Gabala|Azerbaijani_Republic_Shaki|Azerbaijani_Turkey|Bagvalin|Bagvalin_o|Bahun|Bahun_o|Bai|Baiku_Yao_Guizhou|Bajo|Baka|Bakola|Balija|Balkar|Balochi|Balti|Balti_o|Baniya_Gujarat|Baniya_Punjab|Baniya_Uttar_Pradesh_Gupta|Bantu_Kenya|NA|Baoan|Bashkir|Basque_Araba|Basque_Baztan|Basque_Biscay|Basque_French|Basque_Gipuzkoa|Basque_Gipuzkoa_Southwest|Basque_Lower_Navarre|Basque_Navarre_Center|Basque_Navarre_North|Basque_Roncal|Basque_Soule|Basque_Spanish|Batak|BedouinA|BedouinB|Bedzan|Belarusian|BelgianA|BelgianB|BelgianC|Bengali_Bangladesh|Bengali_Bangladesh_SouthEast|Bengali_Bangladesh_Sylhet|Berber_Algeria|Berber_MAR_ERR|Berber_MAR_TIZ|Berber_Tunisia_Chen|Berber_Tunisia_Sen|Besermyan|Bhumihar_Bihar|Bhumij|Biaka|Birhor|Bitonga|Blang|Bolivian_Cochabamba|Bolivian_LaPaz|Bolivian_Pando|Bonan|Bonda|Bosnian|Brahmin_Gujarat|Brahmin_Gujarat_Audichya|Brahmin_Gujarat_Bardai|Brahmin_Gujarat_Nagar|Brahmin_Gujarat_o|Brahmin_Himachal_Pradesh_West|Brahmin_Jammu_Dogra|Brahmin_Karnataka_Tulu|Brahmin_Kerala_Nambudiri|Brahmin_Konkani_Catholic|Brahmin_Kumaon|Brahmin_Manipuri|Brahmin_Rajasthan|Brahmin_Tamil_Nadu|Brahmin_Tamil_Nadu_Iyengar|Brahmin_Tamil_Nadu_Iyer|Brahmin_Telugu|Brahmin_Telugu_Niyogi|Brahmin_Telugu_Vaidiki|Brahmin_UP_Awadh_Saryupareen|Brahmin_UP_Kanyakubja|Brahmin_UP_Lucknow|Brahmin_UP_Lucknow_o|Brahmin_Uttar_Pradesh_East|Brahmin_Uttar_Pradesh_East_o|Brahmin_West_Bengal|Brahui|Bukharian_Jew|Bulala|Bulgarian|Bunt_Kerala|Burmese|Burusho|Buryat|Cachi|Cambodian|Cameroon_Aghem|Cameroon_Bafut|Cameroon_Bakoko|Cameroon_Bangwa|Cameroon_Mbo|Chamalin|Chamar_Uttar_Pradesh|Chamar_Uttar_Pradesh_o|Changana|Changshan_Yao_Guizhou|Chechen|Chenchu|Cherkes|Chipewyan|Chopi|Chukchi|Chuvash|Circassian|Cochin_Jew_A|Cochin_Jew_B|Colla|Cossack_Kuban|Cossack_Ukrainian|Cree|Croatian|Cypriot|Czech|Dai|Damai|Danish|Darginian|Datog|Daur|Dharkar|Dinka|Dolgan|Dong_Guizhou|Dong_Hunan|Dongxiang|Druze|Dungan|Dusadh|Dusun|Dutch|Egyptian|Elmolo|EmiratiA|EmiratiB|EmiratiC|English|English_Cornwall|Eritrean|Erzya|Esan_Nigeria|Eskimo|Eskimo_Chaplin|Eskimo_Naukan|Eskimo_Sireniki|Estonian|Ethiopian_Afar|Ethiopian_Agaw|Ethiopian_Amhara|Ethiopian_Anuak|Ethiopian_Ari|Ethiopian_Ari_blacksmith|Ethiopian_Ari_cultivator|Ethiopian_Gumuz|Ethiopian_Jew|Ethiopian_Mursi|Ethiopian_Oromo|Ethiopian_Tigray|Ethiopian_Wolayta|Even|Evenk|Ezhava|Ezid|Finnish_Central|Finnish_East|Finnish_North|Finnish_Southeast|Finnish_Southwest|French_Alsace|French_Auvergne|French_Bearn|French_Bigorre|French_Brittany|French_Chalosse|French_Corsica|French_Nord|French_Occitanie|French_Paris|French_Provence|French_South|Fulani|Fulani_Ziniare|Gadaba|Gagauz|Gambian|Ganguela|Gelao|Georgian_Ajar|Georgian_Guria|Georgian_Imer|Georgian_Javakheti|Georgian_Jew|Georgian_Kakh|Georgian_Kart|Georgian_Khevs|Georgian_Laz|Georgian_Lechkhumi|Georgian_Megr|Georgian_Meskheti|Georgian_Mtiuleti|Georgian_NorthEast|Georgian_Ratcha|Georgian_Samtckhe|Georgian_Svaneti|Georgian_Tush|Georgian_West|German|German_East|German_Erlangen|German_Hamburg|Gond|Greek_Achaea|Greek_Apulia|Greek_Arcadia|Greek_Argolis|Greek_Cappadocia|Greek_Central_Anatolia|Greek_Central_Macedonia|Greek_Corinthia|Greek_Crete|Greek_Crete_Chania|Greek_Crete_Heraklion|Greek_Crete_Lasithi|Greek_Cyclades_Amorgos|Greek_Cyclades_Kea|Greek_Cyclades_Milos|Greek_Cyclades_Tinos|Greek_Deep_Mani|Greek_Dodecanese|Greek_Dodecanese_Rhodes|Greek_East_Macedonia_and_Thrace|Greek_East_Taygetos|Greek_Elis|Greek_Izmir|Greek_Kos|Greek_Laconia|Greek_Macedonia|Greek_Messenia|Greek_North_Tsakonia|Greek_Peloponnese|Greek_South_Tsakonia|Greek_Thessaly|Greek_Trabzon|Greek_West_Taygetos|Greenlander_East|Greenlander_West|Gujar_Punjab|Gujar_Rajasthan|Gujar_Swat|Gujar_Swat_o|Gujarati|Gujarati_Bharuch_Muslim|Gurung|Hadza|Hakkipikki|Han_Chongqing|Han_Fujian|Han_Guangdong|Han_Guizhou|Han_Henan|Han_Hubei|Han_Jiangsu|Han_Shandong|Han_Shanghai|Han_Shanxi|Han_Sichuan|Han_Zhejiang|Hani|Hawaiian|Hazara|Hezhen|Hinukh|Hmong|Ho|Htin_Mal|Hui|Hui_Guizhou|Huichol|Hungarian|Hunzib|Icelandic|Igbo|Igorot|Indonesian_Bali|Indonesian_Java|Ingrian|Ingushian|Iranian|Iranian_Bandari|Iranian_Fars|Iranian_Jew|Iranian_Lor|Iranian_Mazandarani|Iranian_Persian_Shiraz|Iranian_Zoroastrian|Iraqi|Iraqi_Jew|Iraqw|Irish|Irula|Italian_Abruzzo|Italian_Aosta_Valley|Italian_Apulia|Italian_Basilicata|Italian_Bergamo|Italian_Calabria|Italian_Campania|Italian_Emilia|Italian_Friuli_Venezia_Giulia_Sappada|Italian_Jew|Italian_Lazio|Italian_Liguria|Italian_Lombardy|Italian_Marche|Italian_Molise|Italian_Northeast|Italian_Piedmont|Italian_Trentino_Alto_Adige|Italian_Tuscany|Italian_Umbria|Italian_Veneto|Itelmen|Jamatia|Japanese|Jarawa|Jat_Haryana|Jat_Pahari|Jat_Punjab_Muslim|Jat_Punjab_Sikh|Jat_Uttar_Pradesh|Jehai|Jordanian|Ju_hoan_North|Juang|Kaba|Kabardin|Kadar|Kaitag|Kalash|Kalmyk|Kamboj|Kamboj_o|Kamma|Kanjar|Karachay|Karaite_Egypt|Karakalpak|Karata|Karelian|Karen_Sgaw|Karitiana|Kashmiri_India_Muslim|Kashmiri_Pakistan|Kashmiri_Pakistan_o|Kashmiri_Pandit|Kazakh|Kazakh_China|Kazakh_Xinjiang|Ket|Khakass|Khakass_Kachins|Khamnegan|Khanty|Khatri|Khatri_o|Khmer|Kho_Singanali|Khomani_San|Khonda_Dora|Kikuyu|Kinh_Vietnam|Kirghiz|Kirghiz_China|Knanaya|Kohistani|Koinanbe|Kol|Koli_Gujarat|Komi|Kongo|Konkani_Christian_A|Konkani_Christian_B|Korean|Korean_Antu|Korwa|Koryak|Kosipe|Kshatriya_Uttar_Pradesh_East|Kshatriya_Uttar_Pradesh_East_o|Kubachinian|Kumyk|Kurdish|Kurdish_Jew|Kurichiya|Kurumba|Kusunda|Kuy_Suay|Lahu|Lak|Laka|Lao|Latvian|Lawa|Lebanese_Christian|Lebanese_Druze|Lebanese_Muslim|Lebbo|Lemande|Lezgin|Li|Libyan|Libyan_Jew|Lithuanian_PA|Lithuanian_PZ|Lithuanian_RA|Lithuanian_SZ|Lithuanian_VA|Lithuanian_VZ|Luhya_Kenya|Luo|Luzon|Macedonian|Mada|Madagascar_Mikea|Madagascar_Temoro|Madagascar_Vezo|Madiga|Magar|Makhuwa|Makrani|Mala|Malay|Malayan|Maltese|Manchu_Bijie|Manchu_Jinsha|Manchu_Jinzhou|Manchu_Liaoning|Mandenka|Maniq|Maniyani_Kerala|Mansi|Manyika|Maonan|Maori|Maratha|Mari|Masai|Mayan|Mbuti|Mende_Sierra_Leone|Miao|Miao_Leishan|Miao_Songtao|Mixe|Mixtec|Mlabri|Mogush|Moksha|Moldovan|Moldovan_o|Mon|Mongol_Bijie|Mongol_IMAR|Mongol_Inner_Mongolia|Mongol_Xinjiang|Mongola|Mongolian|Montenegrin|Moroccan|Moroccan_Jew|Moroccan_North|Moroccan_South|Mountain_Jew|Mountain_Jew_o|Mozabite|Mulam|Murut|Mwani|Nahua|Nair|Nanai|Nasoi|Nasrani|Naxi|Ndau|Negidal|Nenets|Nepali_Sherpa_Rolwaling|Nepali_Tamang_Simigaon|Nepali_Tamang_Tashinam|Newar|Nganassan|Ngumba|Nivkh|Nogai|North_Kannadi|North_Ossetian|Norwegian|Nyah_Kur|Nyaneka|Nyanja|Ogiek|Onge|Orcadian|Oroqen|Ossetian|Palestinian|Palestinian_Beit_Sahour|Pallan|Pamiri_Badakhshan|Pamiri_Ishkashim|Pamiri_Rushan|Pamiri_Sarikoli|Pamiri_Sarikoli_China|Pamiri_Shugnan|Pamiri_Wakhi|Paniya|Papuan|Parsi_India|Parsi_Pakistan|Pashtun_Kandahar|Pashtun_Kurram|Pashtun_North_Afghanistan|Pashtun_Tarkalani|Pashtun_Uthmankhel|Pashtun_Yusufzai|Pathan_Bhopal|Piapoco|Pima|Piramalai_Kallar|Poduval_Kerala|Polish|Polish_Kashubian|Polish_Silesian|Portuguese|Pulaya_Kerala|Pulliyar|Pumi|Punjabi_Christian_India|Punjabi_Hindu_India|Punjabi_Lahore|Punjabi_Muslim_India|Punjabi_Sikh_India|Qiang_Danba|Qiang_Daofu|QingYao_Guizhou|Quechua|Rai|Rajput_Garhwal|Rajput_Jammu_Pahari_Pakistan|Rajput_Madhya_Pradesh|Rajput_Potohar|Rajput_Rajasthan|Rajput_Rajasthan_o1|Rajput_Rajasthan_o2|Ratlub|Reddy|Relli|Rendille|Riang|Rohingya|Roma_Balkans|Roma_Barcelona|Roma_Bilbao|Roma_Granada|Roma_Madrid|Roma_Porto|Romanian|Romaniote_Jew|Ronga|Ror|Rumelia_East|Russian_Belgorod|Russian_Kaluga|Russian_Kostroma|Russian_Krasnoborsky|Russian_Kursk|Russian_Leshukonsky|Russian_Orel|Russian_Pinega|Russian_Pinezhsky|Russian_Pskov|Russian_Ryazan|Russian_Smolensk|Russian_Tver|Russian_Voronez|Russian_Yaroslavl|Saami|Saami_Kola|Saharawi|Sakha|Sakilli|Salar|Saliya_Kerala|Samaritan|Sandawe|Santhal|Sardinian|Satnami_Chhattisgarh|Saudi|SaudiA|SaudiB|Scottish|Selkup|Sena|Sengwer|Sephardic_Jew|Sephardic_Jew_o|Serbian|She|Sherpa|Shetlandic|Shor|Shor_Khakassia|Shor_Mountain|Sicilian_East|Sicilian_West|Sindhi|Sindhi_o|Slovakian|Slovenian|Somali|Somali_Kenya|Sorb_Niederlausitz|Spanish_Alacant|Spanish_Andalucia|Spanish_Aragon|Spanish_Aragon_North|Spanish_Asturias|Spanish_Baleares|Spanish_Barcelones|Spanish_Biscay|Spanish_Burgos|Spanish_Camp_de_Tarragona|Spanish_Canarias|Spanish_Cantabria|Spanish_Castello|Spanish_Castilla_La_Mancha|Spanish_Castilla_Y_Leon|Spanish_Cataluna|Spanish_Catalunya_Central|Spanish_Eivissa|Spanish_Extremadura|Spanish_Galicia|Spanish_Girona|Spanish_La_Rioja|Spanish_Lleida|Spanish_Mallorca|Spanish_Menorca|Spanish_Murcia|Spanish_Navarra|Spanish_Pais_Vasco|Spanish_Penedes|Spanish_Pirineu|Spanish_Soria|Spanish_Valencia|Sri_Lankan|Sudanese|Surui|Swedish|Swiss_French|Swiss_German|Swiss_Italian|Syed_Uttar_Pradesh_West|Syrian|Syrian_Jew|Tabasaran|Tai_Lue|Tajik_Ayni|Tajik_Hisor|Tajik_Kulob|Tajik_Yaghnobi|Talysh_Azerbaijan|Tamang|Tamil_Sri_Lanka|Tarkhan_Muslim|Tat_Azerbaijan|Tat_Dagestan_Dzhalgan|Tat_Dagestan_Nyugdi|Tatar_Crimean_steppe|Tatar_Kazan|Tatar_Lipka|Tatar_Mishar|Tatar_Siberian|Tatar_Siberian_Zabolotniye|Telugu|Thai|Tharu|Tharu_o1|Tharu_o2|Thiyya|Tibetan_Chamdo|Tibetan_Gangcha|Tibetan_Gannan|Tibetan_Lhasa|Tibetan_Nagqu|Tibetan_Shannan|Tibetan_Shigatse|Tibetan_Xinlong|Tibetan_Xunhua|Tibetan_Yajiang|Tibetan_Yunnan|Tikar_South|Tindal|Tlingit|Todzin|Tripuri|Tsez_A|Tsez_B|Tswa|Tu|Tubalar|Tujia|Tunisian|Tunisian_Berber_Matmata|Tunisian_Berber_Tamezret|Tunisian_Berber_Zraoua|Tunisian_Douz|Tunisian_Jew|Tunisian_Rbaya|Turkish_Antalya|Turkish_Aydin|Turkish_Balikesir|Turkish_Deliorman|Turkish_Denizli|Turkish_Erzurum|Turkish_Giresun|Turkish_Kayseri|Turkish_Konya|Turkish_Nevsehir|Turkish_Rumeli|Turkish_Sivas|Turkish_Trabzon|Turkmen|Turkmen_Uzbekistan|Tuvinian|Tyagi|Udi|Udmurt|Ukrainian_Chernihiv|Ukrainian_Dnipro|Ukrainian_Lviv|Ukrainian_Rivne|Ukrainian_Sumy|Ukrainian_Zakarpattia|Ukrainian_Zhytomyr|Ukrainian_Zhytomyr_o|Ulchi|Umbundu|Uttar_Pradesh_Scheduled_Castes|Uygur|Uzbek|Vaniya_Kerala|Velama|Vellalar|Vepsian|Vishwakarma_Kerala|Vizayan|Wa|Welsh|Wichi|Xibo|Yadav_Telugu|Yakut|Yao|Yemenite_Al_Bayda|Yemenite_Al_Jawf|Yemenite_Amran|Yemenite_Dhamar|Yemenite_Jew|Yemenite_Mahra|Yi|Yoruba|Yugur|Yukagir_Forest|Yukagir_Tundra|Yukpa|Yuku|Zapotec|Zhuang'
In [16]:
avgs = avgs %>% dplyr::filter(!str_detect(V1,"^(ARG|AUS|BHS|BLZ|BRA|BWA|CAN|CHL|CHN|CMR|COG|CUW|DOM|ETH|GUM|HTI|IDN|IND|JPN|KAZ|KEN|KGZ|KOR|LAO|MEX|MNG|MWI|MYS)"))
avgs = avgs %>% dplyr::filter(!str_detect(V1,"^(NPL|PAK|PAN|PER|PYF|Saka|Sarg|SDN|THA|TJK|TKM|TON|TWN|TZA|UGA|USA|UZB|VEN|VNM|VUT|ZAF)"))
avgs = avgs %>% dplyr::filter(!str_detect(V1,"_o$"))
avgs = avgs %>% dplyr::filter(!str_detect(V1,"low"))
modavgs = modavgs %>% dplyr::filter(!str_detect(V1,"^(Abazin|Abkhasian|Adygei|Aeta|Afrikaner|Agta|Ahiska|Akha|Akhvakh|Alawite|Alevi|Algerian|Altaian|Amerindian|Ami|Andian|Arain)"))
modavgs = modavgs %>% dplyr::filter(!str_detect(V1,"^(Armenian_[AGHP]|Arora|Assyrian|Asur|Atayal|Australian|Awan|Aymara|Azerbaijani_R|Basque_[ABGLR]|Batak|Bedzan|Bengali|Berber_[AM])"))
modavgs = modavgs %>% dplyr::filter(!str_detect(V1,"^(Arora|Assyrian|Asur|Atayal|Australian|Awan|Aymara|Azerbaijani_R|Batak|Bedzan|Bengali|Bagvalin|Bahun|Baiku|Balti|Baniya|Bantu)"))
modavgs = modavgs %>% dplyr::filter(!str_detect(V1,"^(Besermyan|Bhumi|Biaka|Birhor|Bitonga|Blang|Bolivian|Bonan|Bonda|Brahmin|Brahui|Bulala|Bunt|Burmese|Burusho|Buryat|Cachi|Cambodian)"))
modavgs = modavgs %>% dplyr::filter(!str_detect(V1,"^(Cameroon|Chama|Chan|Chen|Chipewyan|Chopi|Chukchi|Chuvash|Circassian|Cochin|Colla|Cree|Dai|Damai|Darginian|Datog|Daur|Dharkar|Dinka)"))
modavgs = modavgs %>% dplyr::filter(!str_detect(V1,"^(Dolgan|Dong|Dungan|Dusadh|Dusun|Elmolo|Eritrean|Esan_Nigeria|Eskimo|Ethiopian|Even|Evenk|Ezhava|Ezid)"))
modavgs = modavgs %>% dplyr::filter(!str_detect(V1,"^(French_Au|French_B[ei]|French_[COP]|Fulani|Gadaba|Gagauz|Gambian|Ganguela|Gelao|Georgian_[GIJKLMRST]|Gond|Greek_[ADEIKLMNSTW])"))
modavgs = modavgs %>% dplyr::filter(!str_detect(V1,"^(Gujar|Gurung|Hadza|Hakkipikki|Han|Hawaiian|Hazara|Hezhen|Hinukh|Hmong|Ho|Htin_Mal|Hui|Hunzib|Igbo|Igorot|Indonesian|Iranian_[BJLMP])"))
modavgs = modavgs %>% dplyr::filter(!str_detect(V1,"^(Iraq|Irula|Italian_[ABEFJLM]|Itelmen|Jamatia|Japanese|Jarawa|Jat|Jehai|Ju_hoan_North|Juang|Kaba|Kadar|Kaitag|Kalash|Kalmyk|Kamboj)"))
modavgs = modavgs %>% dplyr::filter(!str_detect(V1,"^(Irula|Itelmen|Jamatia|Japanese|Jarawa|Jat|Jehai|Ju_hoan_North|Juang|Kaba|Kadar|Kaitag|Kalash|Kalmyk|Kamboj)"))
modavgs = modavgs %>% dplyr::filter(!str_detect(V1,"^(Kamma|Kanjar|Karachay|Karaite_Egypt|Karakalpak|Karata|Karen_Sgaw|Karitiana|Kashmiri|Kazakh|Ket|Khakass|Khamnegan|Khanty|Khatri)"))
modavgs = modavgs %>% dplyr::filter(!str_detect(V1,"^(Khmer|Kho|Kikuyu|Kinh_Vietnam|Kirghiz|Knanaya|Kohistani|Koinanbe|Kol|Komi|Kongo|Konkani|Korean|Korwa|Koryak|Kosipe)"))
modavgs = modavgs %>% dplyr::filter(!str_detect(V1,"^(Kshatriya|Kubachinian|Kumyk|Kurdish|Kurichiya|Kurumba|Kusunda|Kuy_Suay|Lahu|Laka|Lao|Lawa|Lebbo|Lemande|Lezgin|Li|Libyan)"))
modavgs = modavgs %>% dplyr::filter(!str_detect(V1,"^(Lithuanian_[RP]|Luhya_Kenya|Luo|Luzon|Macedonian|Mada|Madagascar|Madiga|Magar|Makhuwa|Makrani|Mala|Malay|Manchu|Mandenka|Maniq)"))
modavgs = modavgs %>% dplyr::filter(!str_detect(V1,"^(Maniyani_Kerala|Mansi|Manyika|Maonan|Maori|Maratha|Mari|Masai|Mayan|Mbuti|Mende_Sierra_Leone|Miao|Mix|Mlabri|Mogush|Mon|Moroccan_)"))
modavgs = modavgs %>% dplyr::filter(!str_detect(V1,"^(Mountain_|Mozabite|Mulam|Murut|Mwani|Nahua|Nair|Nanai|Nasoi|Nasrani|Naxi|Ndau|Negidal|Nenets|Nepali|Newar|Nganassan|Ngumba|Nivkh|Nogai)"))
modavgs = modavgs %>% dplyr::filter(!str_detect(V1,"^(North|Nyah_Kur|Nyan|Ogiek|Onge|Orcadian|Oroqen|Palestinian_|Pallan|Pamiri|Paniya|Papuan|Parsi|Pashtun|Pathan_Bhopal|Piapoco|Pima)"))
modavgs = modavgs %>% dplyr::filter(!str_detect(V1,"^(Piramalai_Kallar|Poduval_Kerala|Polish_|Pul|Pumi|Punj|Qiang|Qing|Quechua|Rai|Raj|Ratlub|Reddy|Relli|Rendille|Riang|Rohingya)"))
modavgs = modavgs %>% dplyr::filter(!str_detect(V1,"^(Roma_|Romaniote|Ronga|Ror|Rumelia_East|Russian_[BKRSTVY]|Saharawi|Sakha|Sakilli|Salar|Saliya_Kerala|Samaritan|Sandawe|Santhal)"))
modavgs = modavgs %>% dplyr::filter(!str_detect(V1,"^(Satnami_Chhattisgarh|Saudi[AB]|Selkup|Sena|Sengwer|She|Shor|Sindhi|Somali|Spanish_[ABCEGLPS]|Sri_Lankan|Sudanese|Surui)"))
modavgs = modavgs %>% dplyr::filter(!str_detect(V1,"^(Syed|Tabasaran|Tai_Lue|Tajik|Talysh_Azerbaijan|Tamang|Tamil_Sri_Lanka|Tarkhan_Muslim|Tat|Telugu|Thai|Tharu|Thiyya|Tibetan)"))
modavgs = modavgs %>% dplyr::filter(!str_detect(V1,"^(Tikar_South|Tindal|Tlingit|Todzin|Tripuri|Tsez|Tswa|Turkish_[ABDEGKNS]|Turkmen|Tuvinian|Tyagi|Udi|Udmurt|Ulchi|Umbundu)"))
modavgs = modavgs %>% dplyr::filter(!str_detect(V1,"^(Uttar|Uygur|Uzbek|Vaniya_Kerala|Velama|Vellalar|Vishwakarma_Kerala|Vizayan|Wa|Welsh|Wichi|Xibo|Yadav_Telugu|Yakut|Yao|Yemenite)"))
modavgs = modavgs %>% dplyr::filter(!str_detect(V1,"^(Yi|Yoruba|Yugur|Yukagir|Yukpa|Yuku|Zapotec|Zhuang)"))
modavgs = modavgs %>% dplyr::filter(!str_detect(V1,"_o$"))
In [17]:
avgs$V1 %>% unique(sort = TRUE)
modavgs$V1 %>% unique(sort = TRUE)
- 'ARM_Areni_C'
- 'ARM_LBA'
- 'ARM_Lchashen_MBA'
- 'ARM_MBA'
- 'AUT_IA_La_Tene'
- 'AUT_LBK_N'
- 'Baltic_EST_BA'
- 'Baltic_EST_IA'
- 'Baltic_EST_MA'
- 'Baltic_EST_Narva'
- 'Baltic_LTU_BA'
- 'Baltic_LTU_Meso'
- 'Baltic_LTU_Narva'
- 'Baltic_LVA_BA'
- 'Baltic_LVA_HG'
- 'Baltic_LVA_MN'
- 'BEL_GoyetQ116-1'
- 'BEL_GoyetQ2'
- 'Bell_Beaker_Bavaria'
- 'Bell_Beaker_CHE'
- 'Bell_Beaker_CZE'
- 'Bell_Beaker_CZE_early'
- 'Bell_Beaker_CZE_late'
- 'Bell_Beaker_England'
- 'Bell_Beaker_England_EBA'
- 'Bell_Beaker_England_highEEF'
- 'Bell_Beaker_England_highWHG'
- 'Bell_Beaker_FRA'
- 'Bell_Beaker_FRA_C'
- 'Bell_Beaker_HUN'
- 'Bell_Beaker_HUN_EBA'
- 'Bell_Beaker_Iberia'
- 'Bell_Beaker_Iberia_C'
- 'Bell_Beaker_ITA'
- 'Bell_Beaker_Mittelelbe-Saale'
- 'Bell_Beaker_Mittelelbe-Saale_contam'
- 'Bell_Beaker_NLD'
- 'Bell_Beaker_POL'
- 'Bell_Beaker_Rhine-Main'
- 'Bell_Beaker_Scotland'
- 'BGR_Bacho_Kiro_MUP'
- 'BGR_Beli_Breyag_EBA'
- 'BGR_C'
- 'BGR_Dzhulyunitsa_N'
- 'BGR_EBA'
- 'BGR_EBA_contam'
- 'BGR_IA'
- 'BGR_Krepost_N'
- 'BGR_Late_C'
- 'BGR_Middle_C'
- 'BGR_MLBA'
- 'BGR_MP_N'
- 'BGR_N'
- 'BGR_Varna_C'
- 'Canary_Islands_Guanche'
- 'Channel_Islands_EIA'
- 'Channel_Islands_IA'
- 'Channel_Islands_LN'
- 'Channel_Islands_MN'
- 'CHE_EBA'
- 'CHE_FN'
- 'CHE_FN_steppe_contam'
- 'CHE_IA'
- 'CHE_LN'
- 'CHE_LN_contam'
- 'CHE_LN_steppe'
- 'CHE_MN'
- 'Corded_Ware_Baltic'
- 'Corded_Ware_Baltic_early'
- 'Corded_Ware_CHE'
- 'Corded_Ware_CZE'
- 'Corded_Ware_CZE_early'
- 'Corded_Ware_CZE_late'
- 'Corded_Ware_CZE_noSteppe'
- 'Corded_Ware_DEU'
- 'Corded_Ware_POL'
- 'Corded_Ware_POL_early'
- 'Corded_Ware_Proto-Unetice_POL'
- 'CZE_Bilina_BA'
- 'CZE_C'
- 'CZE_C_oSteppe'
- 'CZE_Early_Slav'
- 'CZE_EBA_Unetice'
- 'CZE_EE'
- 'CZE_EN_LBK'
- 'CZE_Hallstatt_Bylany'
- 'CZE_IA_Hallstatt'
- 'CZE_IA_La_Tene'
- 'CZE_IA_La_Tene_Hallstatt'
- 'CZE_IA_La_Tene_oFennoscandian'
- 'CZE_Krems_UP'
- 'CZE_LBA_Knoviz'
- 'CZE_LBA_Knoviz_o2'
- 'CZE_LBA_Knoviz_o3'
- 'CZE_LN'
- 'CZE_MBA_Tumulus'
- 'CZE_ME_Baden'
- 'CZE_ME_GAC'
- 'CZE_ME_Rivnac'
- 'CZE_MN'
- 'CZE_N'
- 'CZE_N_oWHG'
- 'CZE_N_possible'
- 'CZE_PE'
- 'CZE_Unetice_C'
- 'CZE_Unetice_EBA'
- 'CZE_Unetice_preC'
- 'CZE_Vestonice16'
- 'DEU_Alberstedt_LN'
- 'DEU_Anselfingen_FN'
- 'DEU_Baalberge_MN'
- 'DEU_BenzigerodeHeimburg_LN'
- 'DEU_Blatterhohle_MN'
- 'DEU_Esperstedt_MN'
- 'DEU_Halberstadt_LBA'
- 'DEU_Karsdorf_LN'
- 'DEU_LBK_HBS'
- 'DEU_LBK_KD'
- 'DEU_LBK_SCH'
- 'DEU_LBK_SMH'
- 'DEU_LBK_UW'
- 'DEU_Lech_BBC'
- 'DEU_Lech_EBA'
- 'DEU_Lech_EBA_contam'
- 'DEU_Lech_MBA'
- 'DEU_MA_ACD_Baiuvaric'
- 'DEU_MA_ACD_Nordic'
- 'DEU_MA_ACD_Ostrogothic'
- 'DEU_MA_Alemannic'
- 'DEU_MA_Alemannic_o1'
- 'DEU_MA_Alemannic_o2'
- 'DEU_MA_Baiuvaric'
- 'DEU_MA_Erfurt1'
- 'DEU_MA_Erfurt2'
- 'DEU_MA_Erfurt3'
- 'DEU_MA_Krakauer_Berg'
- 'DEU_Meso_BDB'
- 'DEU_Meso_TGM'
- 'DEU_Roman'
- 'DEU_Singen_EBA'
- 'DEU_Singen_EIA'
- 'DEU_Tollense_BA'
- 'DEU_Tollense_BA_o2'
- 'DEU_Unetice_EBA'
- 'DEU_Wartberg_MN'
- 'DNK_BA'
- 'DNK_Djursland_SGC'
- 'DNK_LN'
- 'DNK_MN_B'
- 'EGY_Hellenistic_contam'
- 'EGY_Late_Period'
- 'England_C_EBA'
- 'England_C_EBA_highEEF'
- 'England_CA_EBA'
- 'England_EastYorkshire_EIA'
- 'England_EastYorkshire_IA'
- 'England_EastYorkshire_LIA'
- 'England_EastYorkshire_MIA'
- 'England_EastYorkshire_MIA_LIA'
- 'England_EBA'
- 'England_EBA_Bell_Beaker'
- 'England_EBA_highEEF'
- 'England_EIA'
- 'England_EIA_highEEF'
- 'England_EMBA'
- 'England_IA'
- 'England_IA_EarlyMedieval'
- 'England_LBA'
- 'England_LBA_highEEF'
- 'England_LIA'
- 'England_LIA_highEEF'
- 'England_MBA'
- 'England_MBA_highEEF'
- 'England_Mesolithic'
- 'England_MIA'
- 'England_MIA_highEEF'
- 'England_MIA_LIA'
- 'England_N'
- 'England_Roman'
- 'England_Saxon'
- 'England_Trumpington_N'
- 'FIN_Levanluhta_IA'
- 'FRA_Alsace_EBA'
- 'FRA_Alsace_EN'
- 'FRA_Alsace_IA1'
- 'FRA_Alsace_IA2'
- 'FRA_Alsace_LBA'
- 'FRA_Alsace_MN'
- 'FRA_Champagne_EBA'
- 'FRA_Champagne_IA2'
- 'FRA_Champagne_MN'
- 'FRA_EBA'
- 'FRA_EN_PEN'
- 'FRA_ENMN_LBR'
- 'FRA_FN_Lingolsheim_steppe'
- 'FRA_Hauts_De_France_IA2'
- 'FRA_Hauts_De_France_LN'
- 'FRA_Hauts_De_France_MN'
- 'FRA_La_Clape_LN_EBA_Veraza'
- 'FRA_La_Clape_LN_EBA_Veraza_oSteppe'
- ⋯
- 'RUS_Shamanka_EBA'
- 'RUS_Shamanka_N'
- 'RUS_Sidelkino_HG'
- 'RUS_Sintashta_MLBA'
- 'RUS_Sintashta_MLBA_contam'
- 'RUS_Sintashta_MLBA_o1'
- 'RUS_Sintashta_MLBA_o2'
- 'RUS_Sintashta_MLBA_o3'
- 'RUS_Sosonivoy_HG'
- 'RUS_Srubnaya_Alakul_MLBA'
- 'RUS_Srubnaya_MLBA'
- 'RUS_Steppe_Maykop'
- 'RUS_Sunghir'
- 'RUS_Sunghir_MA'
- 'RUS_Tagar'
- 'RUS_Trans-Baikal_BA'
- 'RUS_Trans-Baikal_N'
- 'RUS_Tuva_Aldy_Bel_IA'
- 'RUS_Tyumen_HG'
- 'RUS_Ust_Belaya'
- 'RUS_Ust_Belaya_Angara'
- 'RUS_Ust_Ida_EBA'
- 'RUS_Ust_Ida_LN'
- 'RUS_Ust_Ishim'
- 'RUS_Ust_Kyakhta'
- 'RUS_Veretye_Meso'
- 'RUS_Volga-Kama_N'
- 'RUS_Vologda_Veretye_Meso'
- 'RUS_Vonyuchka_En'
- 'RUS_Yakutia_LUP'
- 'RUS_Yakutia_Ymyiakhtakh_LN'
- 'RUS_Yana_MA'
- 'RUS_Yana_UP'
- 'RUS_Yankovsky_IA'
- 'RUS_Zevakino_Chilikta_IA'
- 'Sarmatian_KAZ'
- 'Sarmatian_KAZ_Aigyrly'
- 'Sarmatian_KAZ_Aktobe'
- 'Sarmatian_KAZ_Bisoba'
- 'Sarmatian_MDA'
- 'Sarmatian_RUS_Caspian_steppe'
- 'Sarmatian_RUS_Caucasus'
- 'Sarmatian_RUS_Pokrovka'
- 'Sarmatian_RUS_Urals'
- 'Sarmatian_Segizsay'
- 'Scotland_C_EBA_highEEF_lc'
- 'Scotland_C_EBA_mediumhighEEF'
- 'Scotland_CA_EBA'
- 'Scotland_EIA'
- 'Scotland_IA'
- 'Scotland_LBA'
- 'Scotland_LIA'
- 'Scotland_MBA'
- 'Scotland_Megalithic'
- 'Scotland_MIA'
- 'Scotland_MIA_LIA'
- 'Scotland_N'
- 'Scotland_Pictish_EMA'
- 'Scotland_Skye_IA'
- 'Scotland_Skye_N'
- 'Scythian_HUN'
- 'Scythian_MDA'
- 'Scythian_RUS_Urals'
- 'Scythian_UKR'
- 'SRB_BA_Maros'
- 'SRB_Iron_Gates_HG'
- 'SRB_Mokrin_EBA_Maros'
- 'SRB_Mokrin_EBA_Maros_oAegean'
- 'SRB_N'
- 'SRB_Starcevo_N'
- 'SVK_EBA'
- 'SVK_IA_Vekerzug'
- 'SVK_LIA'
- 'SVK_LIA_La_Tene'
- 'SVK_Poprad_MA'
- 'SVN_EIA'
- 'SVN_LBA'
- 'SVN_LBA_EIA'
- 'SVN_MBA'
- 'SVN_MIA_oSouth'
- 'SWE_Ajvide_PWC_BAC'
- 'SWE_BA'
- 'SWE_Battle_Axe'
- 'SWE_Hemmor_PWC_BAC'
- 'SWE_IA'
- 'SWE_LN'
- 'SWE_Megalithic_Ansarve'
- 'SWE_Meso'
- 'SWE_Motala_HG'
- 'SWE_Ollsjo_BA'
- 'SWE_PWC_NHG'
- 'SWE_TRB'
- 'SWE_Vasterbjers_PWC_BAC'
- 'SWE_Viking_Age_Sigtuna'
- 'SYR_Ebla_EMBA'
- 'SYR_Tell_Qarassa_Early_Antiquity'
- 'TUR_Alalakh_MLBA'
- 'TUR_Arslantepe_EBA'
- 'TUR_Arslantepe_LC'
- 'TUR_Barcin_C'
- 'TUR_Barcin_N'
- 'TUR_Boncuklu_N'
- 'TUR_Buyukkaya_EC'
- 'TUR_Camlibel_Tarlasi_LC'
- 'TUR_Catalhoyuk_N_Ceramic'
- 'TUR_IA'
- 'TUR_Ikiztepe_LC'
- 'TUR_Isparta_EBA'
- 'TUR_Kaman-Kalehoyuk_MLBA'
- 'TUR_Kumtepe_N'
- 'TUR_Ottoman'
- 'TUR_Ovaoren_EBA'
- 'TUR_Pinarbasi_HG'
- 'TUR_Tell_Kurdu_EC'
- 'TUR_Tell_Kurdu_MC'
- 'TUR_Tepecik_Ciftlik_N'
- 'TUR_Titris_Hoyuk_EBA'
- 'UKR_Catacomb'
- 'UKR_Chernyakhiv_Legedzine'
- 'UKR_Chernyakhiv_Shyshaky'
- 'UKR_Cimmerian'
- 'UKR_Dereivka_I_En1'
- 'UKR_Dereivka_I_En2'
- 'UKR_EBA'
- 'UKR_Globular_Amphora'
- 'UKR_MBA'
- 'UKR_Meso'
- 'UKR_N'
- 'UKR_Srubnaya_MLBA'
- 'UKR_Trypillia'
- 'UKR_Trypillia_En'
- 'VK2020_DNK_Funen_VA'
- 'VK2020_DNK_Jutland_IA'
- 'VK2020_DNK_Jutland_VA'
- 'VK2020_DNK_Langeland_VA'
- 'VK2020_DNK_Sealand_EVA'
- 'VK2020_DNK_Sealand_IA'
- 'VK2020_DNK_Sealand_LNBA'
- 'VK2020_DNK_Sealand_VA'
- 'VK2020_England_Dorset_VA'
- 'VK2020_England_Oxford_VA'
- 'VK2020_EST_Saaremaa_EVA'
- 'VK2020_Faroes_EM'
- 'VK2020_Faroes_VA'
- 'VK2020_GreenlandE_VA'
- 'VK2020_GreenlandW_VA'
- 'VK2020_IRL_Dublin_VA'
- 'VK2020_IRL_Eyrephort_VA'
- 'VK2020_ISL_Hofstadir_VA'
- 'VK2020_ISL_Hringsdalur_VA'
- 'VK2020_ISL_Ingiridarstadir_VA'
- 'VK2020_Isle_Of_Man_VA'
- 'VK2020_ITA_Foggia_MA'
- 'VK2020_NOR_Mid_IA'
- 'VK2020_NOR_Mid_MA'
- 'VK2020_NOR_Mid_VA'
- 'VK2020_NOR_North_IA'
- 'VK2020_NOR_North_LN_HG'
- 'VK2020_NOR_North_VA'
- 'VK2020_NOR_North_VA_o1'
- 'VK2020_NOR_North_VA_o2'
- 'VK2020_NOR_South_IA'
- 'VK2020_NOR_South_VA'
- 'VK2020_POL_Bodzia_VA'
- 'VK2020_POL_Cedynia_MA'
- 'VK2020_POL_Cedynia_VA'
- 'VK2020_POL_Krakow_MA'
- 'VK2020_POL_Sandomierz_VA'
- 'VK2020_RUS_Gnezdovo_VA'
- 'VK2020_RUS_Kurevanikha_VA'
- 'VK2020_RUS_Ladoga_VA'
- 'VK2020_RUS_Pskov_VA'
- 'VK2020_Scotland_Orkney_VA'
- 'VK2020_SWE_Gotland_VA'
- 'VK2020_SWE_Karda_VA'
- 'VK2020_SWE_Malmo_VA'
- 'VK2020_SWE_Oland_EVA'
- 'VK2020_SWE_Oland_IA'
- 'VK2020_SWE_Oland_VA'
- 'VK2020_SWE_Skara_VA'
- 'VK2020_SWE_Uppsala_VA'
- 'VK2020_UKR_Lutsk_MA'
- 'VK2020_UKR_Shestovitsa_VA'
- 'VK2020_Wales_Anglesey_VA'
- 'Wales_CA_EBA'
- 'Wales_IA'
- 'Wales_LBA'
- 'Wales_MBA'
- 'Wales_Meso'
- 'Wales_MIA'
- 'Wales_MIA_LIA'
- 'Wales_N'
- 'WHG'
- 'Yamnaya_BGR'
- 'Yamnaya_KAZ_Karagash'
- 'Yamnaya_KAZ_Mereke'
- 'Yamnaya_RUS_Caucasus'
- 'Yamnaya_RUS_Kalmykia'
- 'Yamnaya_RUS_Samara'
- 'Yamnaya_UKR'
- 'Albanian'
- 'Armenian_Erzurum'
- 'Armenian_Syunik'
- 'Armenian_Urfa'
- 'Ashkenazi_Belarussia'
- 'Ashkenazi_Germany'
- 'Ashkenazi_Lithuania'
- 'Ashkenazi_Poland'
- 'Ashkenazi_Russia'
- 'Ashkenazi_Ukraine'
- 'Austrian'
- 'Avar'
- 'Azerbaijani_Dagestan'
- 'Azerbaijani_Iran'
- 'Azerbaijani_Turkey'
- 'Bai'
- 'Bajo'
- 'Baka'
- 'Bakola'
- 'Balija'
- 'Balkar'
- 'Balochi'
- 'Baoan'
- 'Bashkir'
- 'Basque_French'
- 'Basque_Navarre_Center'
- 'Basque_Navarre_North'
- 'Basque_Soule'
- 'Basque_Spanish'
- 'BedouinA'
- 'BedouinB'
- 'Belarusian'
- 'BelgianA'
- 'BelgianB'
- 'BelgianC'
- 'Berber_Tunisia_Chen'
- 'Berber_Tunisia_Sen'
- 'Bosnian'
- 'Bukharian_Jew'
- 'Bulgarian'
- 'Chechen'
- 'Cherkes'
- 'Cossack_Kuban'
- 'Cossack_Ukrainian'
- 'Croatian'
- 'Cypriot'
- 'Czech'
- 'Danish'
- 'Druze'
- 'Dutch'
- 'Egyptian'
- 'EmiratiA'
- 'EmiratiB'
- 'EmiratiC'
- 'English'
- 'English_Cornwall'
- 'Erzya'
- 'Estonian'
- 'Finnish_Central'
- 'Finnish_East'
- 'Finnish_North'
- 'Finnish_Southeast'
- 'Finnish_Southwest'
- 'French_Alsace'
- 'French_Brittany'
- 'French_Nord'
- 'French_Seine-Maritime'
- 'French_South'
- 'Georgian_Ajar'
- 'Georgian_NorthEast'
- 'Georgian_West'
- 'German'
- 'German_East'
- 'German_Erlangen'
- 'German_Hamburg'
- 'Greek_Cappadocia'
- 'Greek_Central_Anatolia'
- 'Greek_Central_Macedonia'
- 'Greek_Corinthia'
- 'Greek_Crete'
- 'Greek_Crete_Chania'
- 'Greek_Crete_Heraklion'
- 'Greek_Crete_Lasithi'
- 'Greek_Cyclades_Amorgos'
- 'Greek_Cyclades_Kea'
- 'Greek_Cyclades_Milos'
- 'Greek_Cyclades_Tinos'
- 'Greek_Peloponnese'
- 'Greenlander_East'
- 'Greenlander_West'
- 'Hungarian'
- 'Icelandic'
- 'Ingrian'
- 'Ingushian'
- 'Iranian'
- 'Iranian_Fars'
- 'Iranian_Zoroastrian'
- 'Irish'
- 'Italian_Calabria'
- 'Italian_Campania'
- 'Italian_Northeast'
- 'Italian_Piedmont'
- 'Italian_Trentino_Alto_Adige'
- 'Italian_Tuscany'
- 'Italian_Umbria'
- 'Italian_Veneto'
- 'Jordanian'
- 'Karelian'
- 'Lak'
- 'Latvian'
- 'Lebanese_Christian'
- 'Lebanese_Druze'
- 'Lebanese_Muslim'
- 'Maltese'
- 'Moksha'
- 'Moldovan'
- 'Moroccan'
- 'Norwegian'
- 'Ossetian'
- 'Palestinian'
- 'Polish'
- 'Portuguese'
- 'Romanian'
- 'Russian_Leshukonsky'
- 'Russian_Orel'
- 'Russian_Pinega'
- 'Russian_Pinezhsky'
- 'Russian_Pskov'
- 'Saami'
- 'Saami_Kola'
- 'Sardinian'
- 'Saudi'
- 'Scottish'
- 'Sephardic_Jew'
- 'Serbian'
- 'Sicilian_East'
- 'Sicilian_West'
- 'Slovakian'
- 'Slovenian'
- 'Sorb_Niederlausitz'
- 'Spanish_Mallorca'
- 'Spanish_Menorca'
- 'Spanish_Murcia'
- 'Spanish_Navarra'
- 'Spanish_Terres_de_l\'Ebre'
- 'Spanish_Valencia'
- 'Swedish'
- 'Swiss_French'
- 'Swiss_German'
- 'Swiss_Italian'
- 'Syrian'
- 'Syrian_Jew'
- 'Tarkhan_Sikh/Hindu'
- 'Tu'
- 'Tubalar'
- 'Tujia'
- 'Tunisian'
- 'Tunisian_Berber_Matmata'
- 'Tunisian_Berber_Tamezret'
- 'Tunisian_Berber_Zraoua'
- 'Tunisian_Douz'
- 'Tunisian_Jew'
- 'Tunisian_Rbaya'
- 'Turkish_Rumeli'
- 'Turkish_Trabzon'
- 'Ukrainian_Chernihiv'
- 'Ukrainian_Dnipro'
- 'Ukrainian_Lviv'
- 'Ukrainian_Rivne'
- 'Ukrainian_Sumy'
- 'Ukrainian_Zakarpattia'
- 'Ukrainian_Zhytomyr'
- 'Vepsian'
In [18]:
myavgs = avgs %>% select(-V1)
row.names(myavgs) = avgs$V1
mymodavgs = modavgs %>% select(-V1)
row.names(mymodavgs) = modavgs$V1
Warning message: “Setting row names on a tibble is deprecated.” Warning message: “Setting row names on a tibble is deprecated.”
Combine all data
In [19]:
allavgs = bind_rows(myavgs,mymodavgs)
Find nearest neighbors for each row
In [27]:
mynn = kNN(allavgs,k = nrow(allavgs)-1)
mynn
k-nearest neighbors for 995 objects (k=994). Available fields: dist, id, k, sort
In [28]:
mynn = rownames_to_column(as.data.frame(mynn$id)) %>% as_tibble() %>% mutate(`0` = row_number(),.after = rowname)
In [29]:
mynn %>% sample_n(10)
| rowname | 0 | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | ⋯ | 985 | 986 | 987 | 988 | 989 | 990 | 991 | 992 | 993 | 994 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| <chr> | <int> | <int> | <int> | <int> | <int> | <int> | <int> | <int> | <int> | ⋯ | <int> | <int> | <int> | <int> | <int> | <int> | <int> | <int> | <int> | <int> |
| VK2020_GreenlandE_VA | 767 | 765 | 940 | 914 | 870 | 802 | 772 | 771 | 758 | ⋯ | 978 | 559 | 656 | 598 | 554 | 586 | 236 | 237 | 841 | 840 |
| VK2020_SWE_Karda_VA | 797 | 19 | 756 | 887 | 168 | 23 | 163 | 175 | 305 | ⋯ | 978 | 559 | 656 | 598 | 554 | 586 | 236 | 237 | 841 | 840 |
| Iberia_East_IA | 332 | 345 | 342 | 849 | 341 | 851 | 848 | 349 | 890 | ⋯ | 559 | 656 | 653 | 554 | 598 | 586 | 236 | 237 | 841 | 840 |
| Sarmatian_KAZ_Bisoba | 661 | 666 | 663 | 659 | 665 | 667 | 310 | 660 | 662 | ⋯ | 638 | 598 | 656 | 554 | 586 | 978 | 236 | 237 | 841 | 840 |
| RUS_Sidelkino_HG | 625 | 648 | 582 | 649 | 622 | 650 | 780 | 583 | 749 | ⋯ | 571 | 838 | 564 | 656 | 236 | 554 | 978 | 237 | 841 | 840 |
| BGR_EBA | 45 | 517 | 276 | 424 | 30 | 42 | 461 | 46 | 411 | ⋯ | 559 | 653 | 656 | 554 | 598 | 586 | 236 | 237 | 841 | 840 |
| Spanish_Menorca | 964 | 352 | 967 | 963 | 968 | 965 | 944 | 925 | 415 | ⋯ | 559 | 653 | 656 | 554 | 598 | 586 | 236 | 237 | 841 | 840 |
| Swiss_German | 971 | 888 | 886 | 857 | 856 | 447 | 408 | 305 | 351 | ⋯ | 638 | 559 | 656 | 598 | 554 | 586 | 236 | 237 | 841 | 840 |
| HUN_North_Transdanubia | 310 | 661 | 666 | 660 | 663 | 667 | 665 | 659 | 658 | ⋯ | 638 | 598 | 656 | 978 | 554 | 586 | 236 | 237 | 841 | 840 |
| HUN_Avar_Middle-Late_Danube-Tisza | 273 | 268 | 594 | 285 | 263 | 563 | 645 | 272 | 643 | ⋯ | 137 | 468 | 811 | 174 | 219 | 512 | 384 | 429 | 841 | 840 |
Pivot and clean up the data
In [30]:
mynames = mynn %>% select(rowname) %>% mutate(val = row_number())
In [31]:
mynn = mynn %>% pivot_longer(cols = matches("^\\d"),names_to = "rank",values_to = "val") %>% inner_join(mynames,by = "val") %>% select(c(1,4,2))
In [32]:
colnames(mynn) = c("target","population","distance")
mynn = mynn %>% dplyr::filter(distance %in% 1:5)
In [33]:
mynn %>% sample_n(10)
| target | population | distance |
|---|---|---|
| <chr> | <chr> | <chr> |
| Turkish_Trabzon | Greek_Cappadocia | 4 |
| IRN_Hajji_Firuz_C | Turkish_Trabzon | 4 |
| BelgianB | French_Nord | 1 |
| Danish | VK2020_DNK_Sealand_VA | 3 |
| BelgianC | Swiss_German | 4 |
| Swedish | VK2020_SWE_Skara_VA | 4 |
| Russian_Pskov | DEU_MA_Krakauer_Berg | 3 |
| HUN_Starcevo_N | HUN_LBK_MN | 3 |
| Moksha | Ingrian | 3 |
| HRV_Pop_RomanP | SVK_LIA | 5 |
In [34]:
write_csv(mynn,"../Genetics/G25/Data/CSV/top_10_dist_all.csv")
In [35]:
mynn %>% dplyr::filter(str_detect(target,"^Ukrainian.+[^o]$"))
| target | population | distance |
|---|---|---|
| <chr> | <chr> | <chr> |
| Ukrainian_Chernihiv | Ukrainian_Rivne | 1 |
| Ukrainian_Chernihiv | Ukrainian_Dnipro | 2 |
| Ukrainian_Chernihiv | Ukrainian_Sumy | 3 |
| Ukrainian_Chernihiv | Ukrainian_Zhytomyr | 4 |
| Ukrainian_Chernihiv | Russian_Orel | 5 |
| Ukrainian_Lviv | Ukrainian_Zakarpattia | 1 |
| Ukrainian_Lviv | Polish | 2 |
| Ukrainian_Lviv | Ukrainian_Sumy | 3 |
| Ukrainian_Lviv | Ukrainian_Zhytomyr | 4 |
| Ukrainian_Lviv | Ukrainian_Rivne | 5 |
| Ukrainian_Rivne | Ukrainian_Chernihiv | 1 |
| Ukrainian_Rivne | Ukrainian_Zhytomyr | 2 |
| Ukrainian_Rivne | Ukrainian_Dnipro | 3 |
| Ukrainian_Rivne | Polish | 4 |
| Ukrainian_Rivne | DEU_MA_Krakauer_Berg | 5 |
| Ukrainian_Sumy | Ukrainian_Chernihiv | 1 |
| Ukrainian_Sumy | Russian_Orel | 2 |
| Ukrainian_Sumy | Ukrainian_Rivne | 3 |
| Ukrainian_Sumy | Ukrainian_Zhytomyr | 4 |
| Ukrainian_Sumy | Ukrainian_Dnipro | 5 |
| Ukrainian_Zakarpattia | Ukrainian_Lviv | 1 |
| Ukrainian_Zakarpattia | Croatian | 2 |
| Ukrainian_Zakarpattia | Hungarian | 3 |
| Ukrainian_Zakarpattia | Slovakian | 4 |
| Ukrainian_Zakarpattia | Slovenian | 5 |
| Ukrainian_Zhytomyr | Ukrainian_Rivne | 1 |
| Ukrainian_Zhytomyr | Ukrainian_Chernihiv | 2 |
| Ukrainian_Zhytomyr | Ukrainian_Sumy | 3 |
| Ukrainian_Zhytomyr | Polish | 4 |
| Ukrainian_Zhytomyr | Ukrainian_Dnipro | 5 |
In [36]:
mynn$distance = as.numeric(scale(as.numeric(mynn$distance)))
In [37]:
myg = graph_from_data_frame(mynn)
In [38]:
myg
IGRAPH b80b3be DN-- 995 4975 -- + attr: name (v/c), distance (e/n) + edges from b80b3be (vertex names): [1] ARM_Areni_C ->Levant_Megiddo_MLBA_o1 [2] ARM_Areni_C ->Armenian_Syunik [3] ARM_Areni_C ->ARM_LBA [4] ARM_Areni_C ->Ostrogothic_Crimea_ACD [5] ARM_Areni_C ->Greek_Cappadocia [6] ARM_LBA ->ARM_MBA [7] ARM_LBA ->ARM_Lchashen_MBA [8] ARM_LBA ->RUS_Alan_MA + ... omitted several edges
In [39]:
myg = as_tbl_graph(myg) %>% mutate(c_auth = centrality_authority(weights = distance))
myg
# A tbl_graph: 995 nodes and 4975 edges # # A directed simple graph with 1 component # # A tibble: 995 × 2 name c_auth <chr> <dbl> 1 ARM_Areni_C 0 2 ARM_LBA 1.16e- 9 3 ARM_Lchashen_MBA 0 4 ARM_MBA 0 5 AUT_IA_La_Tene 7.69e- 6 6 AUT_LBK_N 7.31e-11 # ℹ 989 more rows # # A tibble: 4,975 × 3 from to distance <int> <int> <dbl> 1 1 502 -1.41 2 1 825 -0.707 3 1 2 0 # ℹ 4,972 more rows
In [40]:
myg %>% select(name,c_auth) %>% as.data.frame() %>% arrange(desc(c_auth))
| name | c_auth |
|---|---|
| <chr> | <dbl> |
| England_CA_EBA | 1.000000000 |
| Bell_Beaker_England | 0.173952611 |
| England_LIA | 0.116812306 |
| England_MBA | 0.109148862 |
| Corded_Ware_CHE | 0.089944309 |
| ISL_Viking_Age_Pre_Christian | 0.081853731 |
| Bell_Beaker_NLD | 0.051372059 |
| Scottish | 0.051015268 |
| SWE_Ollsjo_BA | 0.049313911 |
| POL_Chlopice_Vesele_Culture | 0.046520461 |
| CZE_Unetice_EBA | 0.033693051 |
| Bell_Beaker_CZE_late | 0.029849571 |
| England_EastYorkshire_LIA | 0.029163725 |
| Scotland_LIA | 0.028726403 |
| CZE_Unetice_preC | 0.027456141 |
| Scotland_LBA | 0.025179970 |
| England_MIA_LIA | 0.024486887 |
| England_LBA | 0.024417841 |
| VK2020_DNK_Sealand_VA | 0.023105356 |
| VK2020_SWE_Skara_VA | 0.021617028 |
| England_EIA | 0.021563486 |
| CZE_Bilina_BA | 0.016005905 |
| VK2020_NOR_North_VA | 0.014743177 |
| VK2020_IRL_Eyrephort_VA | 0.010155855 |
| Bell_Beaker_Bavaria | 0.009698243 |
| Scotland_EIA | 0.009426029 |
| English | 0.008341500 |
| England_Saxon | 0.007196527 |
| SWE_LN | 0.006523234 |
| VK2020_EST_Saaremaa_EVA | 0.006340086 |
| ⋮ | ⋮ |
| Lebanese_Muslim | 0 |
| Maltese | 0 |
| Norwegian | 0 |
| Ossetian | 0 |
| Palestinian | 0 |
| Portuguese | 0 |
| Russian_Pinega | 0 |
| Russian_Pinezhsky | 0 |
| Russian_Pskov | 0 |
| Saami | 0 |
| Sardinian | 0 |
| Saudi | 0 |
| Sephardic_Jew | 0 |
| Slovenian | 0 |
| Sorb_Niederlausitz | 0 |
| Spanish_Murcia | 0 |
| Swedish | 0 |
| Swiss_French | 0 |
| Tarkhan_Sikh/Hindu | 0 |
| Tu | 0 |
| Tunisian | 0 |
| Tunisian_Berber_Matmata | 0 |
| Tunisian_Jew | 0 |
| Turkish_Rumeli | 0 |
| Turkish_Trabzon | 0 |
| Ukrainian_Chernihiv | 0 |
| Ukrainian_Dnipro | 0 |
| Ukrainian_Rivne | 0 |
| Ukrainian_Zhytomyr | 0 |
| Vepsian | 0 |
In [41]:
options(repr.plot.width = 26,repr.plot.height = 30,repr.plot.res = 400,repr.plot.bg = "gray20")
In [42]:
#myp = myg %>% ggraph(layout = 'unrooted')#,circular = TRUE)
myp = myg %>% ggraph(layout = 'stress',circular = TRUE)
myp + geom_edge_fan(aes(color = distance,alpha = after_stat(index),start_cap = label_rect(node1.name),end_cap = label_rect(node2.name)),strength = 1.25,edge_width = 0.15) +
geom_node_label(aes(label = name),label.size = 0,size = 1,alpha = 0.6,fill = "gray15",color = "gray75") + #,repel = TRUE,max.overlaps = 10) +
scale_edge_alpha('Edge direction') +
scale_edge_color_gradient2("distance",low = "cyan",mid = "snow",high = "orange") +
theme_void() +
theme(plot.background = element_rect("gray20"),legend.title = element_text(color = "snow"),legend.text = element_text(color = "snow"),legend.position = "bottom") +
guides(edge_alpha = guide_edge_direction()) +
coord_flip()
Warning message:
“Using the `size` aesthetic in this geom was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` in the `default_aes` field and elsewhere instead.”